When he arrived in the United States at the age of 18, he was placed in a Jewish orphanage where he created a stir by challenging the kashrut of the institution since the supervising rabbi did not have a beard and, more importantly, was not fluent in the commentaries of the Pri Megadim by Rabbi Yoseph Te'omim.[citation needed] This was a standard for Rabbis in Europe. A social worker introduced him to Saul Lieberman, a leading Talmudist at the Jewish Theological Seminary of America (JTS) in New York, who recognized his brilliance and took him under his wing. Weiss studied with Lieberman for many years at the JTS.

He married Zipporah Hager, a descendant of the Vizhnitzer Rebbes. They had 3 children: Baruch (formally known as Bernard), Ephraim, and Yeshiahu. He has six grandchildren, all of whom are scholars as well; Avidan, Hadar, Daniel, Rebecca, Benjamin, and Eliana.

Weiss later changed his name to "Halivni," a Hebrew translation for "weiss" or "white." He originally wanted to abandon the surname Weiss because that was the name of a guard in the concentration camp in which he was interned. He initially considering changing his name to Halivni; however, out of respect for this grandfather/teacher Yeshayahu Weiss, he maintained a memory of the family name, using the compound name Weiss Halivni.[citation needed]

Halivni is the author of Mekorot u'Mesorot, a projected ten volume commentary on the Talmud. He is also the author of the English language volumes Peshat and Derash, Revelation Restored, his memoirs The Book and the Sword and others. Halivni also served as Littauer Professor of Talmud and Classical Rabbinics in the Department of Religion at Columbia University.

Halivni's source-critical approach to Talmud study has had a major impact on academic understanding and study of the Talmud.[3] The traditional understanding viewed the Talmud as a unified homogeneous work. While other scholars had also treated the Talmud as a multi-layered work, Halivni's innovation (primarily in the second volume of his Mekorot u-Mesorot) was to distinguish between the onymous statements, which are generally succinct Halachic rulings or inquiries attributed to known Amoraim, and the anonymous statements, characterised by a much longer analysis often consisting of lengthy dialectic discussion, which he attributed to the later authors- "Stamma'im" (or Savora'im).

His methodology of source-critical analysis of the Talmud is controversial among most Orthodox Jews, but is accepted in the non-Orthodox Jewish community, and by some within Modern Orthodoxy. Halivni terms the anonymous texts of the Talmud as having been said by Stammaim (based on the phrase " stama d'talmuda" which refers to the anonymous material in the Gemara), who lived after the period of the Amoraim, but before the Geonic period. He posits that these Stammaim were the recipients of terse Tannaitic and Amoraic statements and that they endeavored to fill in the reasoning and argumentative background to such apodictic statements.

The methodology employed in his commentary Mekorot u' Mesorot attempts to give Halivni's analysis of the correct import and context and demonstrates how the Talmudic Stammaim often erred in their understanding of the original context.

In Halivni's books Peshat and Derash and Revelation Restored, he attempts to harmonize biblical criticism with traditional religious belief using a concept he developed termed Chate'u Israel (literally, "Israel has sinned"). This concept states that the biblical texts originally given to Moses have become irretrievably corrupted. Revelation Restored writes as follows:

According to the biblical account itself, the people of Israel forsook the Torah, in the dramatic episode of the golden calf, only forty days after the revelation at Sinai. From that point on, until the time of Ezra, the scriptures reveal that the people of Israel were steeped in idolatry and negligent of the Mosaic law. Chate'u Yisrael, states that in the period of neglect and syncretism after the conquest of Canaan when the originally monotheistic Israelites adopted pagan practices from their neighbours, the Torah of Moses became "blemished and maculated."

According to Halivni, this process continued until the time of Ezra (c.450 BCE), when finally, upon their return from Babylon, the people accepted the Torah. It was at that time that the previously rejected, and therefore maculated, text of the Torah was recompiled and edited by Ezra and his “entourage.” He claims that this is attested in the books of Ezra and Nehemiah, and Halivni supports his theory with Talmudic and Midrashic sources which indicate that Ezra played a role in editing the Torah. He further states that while the text of the Pentateuch was corrupted, oral tradition preserved intact many of the laws, which is why the Oral Law appears to contradict the Biblical text in certain details.

This view was seen as possibly being in contradiction to the 8th of Maimonides' 13 principles of faith, which states "the Torah that we have today is the one that was dictated to Moses by God". Some believe that Maimonides says that this applies to every single word in the Torah. As a result, Halivni's assertions were rejected by some Orthodox rabbis.[5]

Halivni was involved in the 1983 controversy at JTS surrounding the training and ordination of women as rabbis.[1] He felt that there may be halakhic methods for ordaining women as rabbis, but that more time was needed before such could be legitimately instituted, and that the decision had been made as a policy decision by the governing body of the Seminary rather than as a psak halachah within the traditional rabbinic legal process. This disagreement led to his break with the seminary and with the movement of Conservative Judaism, and to his co-founding of the Union for Traditional Judaism.[citation needed]

Until 2005, Halivni was the spiritual leader of Kehilat Orach Eliezer, a congregation on Manhattan's Upper West Side, a position he had held since the congregation's foundation in 1992.[6] In 2002, many members of the congregation wanted to allow women to be called up to the Torah, which, while supported by a then-recent legal argument by Rabbi Mendel Shapiro, is opposed by many rabbis for halakhic and sociological reasons.[citation needed] Halivni was not excited about the practice, and told the congregation: "I shall allow it, but only if it is done no more frequently than a few times a year, and only if it is done in a separate room from the ‘real’ service." Thus, the congregation allows this practice only under very limited circumstances.[citation needed] Nevertheless, even this “compromise” was far too liberal for many congregants. On the other side, many liberals favored a Partnership minyan approach and were frustrated by KOE's failure to include women in the main Torah service.[citation needed]

Breaking the Tablets: Jewish Theology After the Shoah, a collection of essays on Holocaust theology.

The central thesis of “Breaking the Tablets” is that the history of the Jews is “bookmarked” by two diametrically opposing “revelations”: Sinai and Auschwitz. The revelation on Mount Sinai was the apex of God’s nearness to the Jews, while the revelation at Auschwitz was the nadir of God’s absence from them. Halivni’s conviction is that Auschwitz represents not merely God’s “hiding his face” from Israel, as a consequence of the Jews’ sins — a familiar trope in rabbinic theology — but also his actual, ontological withdrawal from human history.[10]

In Breaking the Tablets Halivni explicitly rejected the notion that this withdrawal is simply an example of "God hiding his face" as viewed in normative Judaism. The concept of hester panim (God's hiding his face) is classically used with regard to punishment, and Halivni is adamant that the Holocaust cannot in any way be regarded as a punishment for Israel's sins.